From: Sharlatan Hellseher <sharlatanus@gmail.com>
To: Vinicius Monego <monego@posteo.net>
Cc: 48046@debbugs.gnu.org
Subject: [bug#48046] [PATCH]: Gnu add astropy
Date: Sat, 22 May 2021 20:00:35 +0000 [thread overview]
Message-ID: <CAO+9K5oVE-z7giCse5ZSZq0JL=MPwS5zsnYAW-EF46a2CjC3Fg@mail.gmail.com> (raw)
In-Reply-To: <a2c650067b52001a3b205cbc1b3999eb99ea4d92.camel@posteo.net>
[-- Attachment #1: Type: text/plain, Size: 3919 bytes --]
Hi Vinicius,
My attempt to make Astropy test working failed as well. the project
heavily depends on TOX which requires pip to install missing
dependencies for itself. I run test with pytest but it looks like it's
not allowed by this
https://github.com/astropy/astropy/blob/main/astropy/__init__.py#L139
I'll come back to conquer it once again when I have some fresh ideas.
On Wed, 19 May 2021 at 18:16, Vinicius Monego <monego@posteo.net> wrote:
>
> Hi,
>
> Em seg, 2021-04-26 às 20:01 +0000, Sharlatan Hellseher escreveu:
> > Hi Guix team!
> >
> > Here is my attempt to pack bulky python package -
> > https://www.astropy.org/
> > I've disabled test and add minor modification removing `_compiler.c'
> > file.
>
> I've tried to package AstroPy before but got stuck in the dependencies,
> more specifically pytest-astropy. There is a bug somewhere that pytest-
> filter-subpackage is not found by setup.py, even though it's listed in
> the inputs. I encountered that problem again here, after enabling the
> tests.
>
> > + ;; NOTE: (Sharlatan-20210426T204315+0100): Tests require build
> > astropy
> > + ;; module, it needs a good review on how to enable them.
> > + `(#:tests? #f
>
> AstroPy uses pytest, which is not listed in your native-inputs. The
> other dependencies I had to add are python-hypothesis, python-pytest-
> cov, python-pytest-astropy and python-pytest-xdist. According to the
> documentation, it should be as simple as running pytest to run the
> entire test suite:
>
> https://docs.astropy.org/en/latest/development/testguide.html#running-tests
>
> If you end up in 'ModuleNotFoundError: No module named "astropy"', you
> may have to update PYTHONPATH after the install phase with (add-
> installed-pythonpath inputs outputs). That usually happens when
> replacing the check phase.
>
> > + (inputs
> > + `(("asdf" ,python-asdf)
> > + ("beautifulsoup4" ,python-beautifulsoup4)
> > + ("bleach" ,python-bleach)
> > + ("bottleneck" ,python-bottleneck)
> > + ("cfitsio" ,cfitsio)
> > + ("dask" ,python-dask)
> > + ("expat" ,expat)
> > + ("graphviz" ,graphviz)
> > + ("h5py" ,python-h5py)
> > + ("html5lib" ,python-html5lib)
> > + ("jplephem" ,python-jplephem)
> > + ("matplotlib" ,python-matplotlib)
> > + ("mpmath" ,python-mpmath)
> > + ("numpy" ,python-numpy)
> > + ("pandas" ,python-pandas)
> > + ("pyerfa" ,python-pyerfa)
> > + ("pytz" ,python-pytz)
> > + ("pyyaml" ,python-pyyaml)
> > + ("scipy" ,python-scipy)
> > + ("sortedcontainers" ,python-sortedcontainers)
> > + ("wcslib" ,wcslib)))
>
> AstroPy is a library, its Python inputs should be propagated here.
> See https://guix.gnu.org/manual/en/html_node/package-Reference.html#package-Reference
> for reference.
>
> Also, the documentation states that the only strict requirements are
> PyERFA and NumPy:
>
> https://docs.astropy.org/en/stable/install.html
>
> IMO we should only propagate these, and leave the rest in native-inputs
> as needed by tests.
>
> Now speaking of the astropy dependencies, pytest-astropy is supposed to
> propagate its six dependencies. AFAIK its purpose is to be a
> metapackage to install these other 6 pytest modules. PyERFA should also
> propagate numpy (liberfa can remain as normal input).
>
> I'll take a look at this package again next week. Could you test these
> suggestions in the meantime?
>
> Vinicius
>
>
--
… наш разум - превосходная объяснительная машина которая способна
найти смысл почти в чем угодно, истолковать любой феномен, но
совершенно не в состоянии принять мысль о непредсказуемости.
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From 4b0d8e20915ee674054cb3bd1b3573a9f42bd08a Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Sat, 22 May 2021 20:52:49 +0100
Subject: [PATCH] gnu: astropy: rc1
* gnu/packages/astronomy.scm (python-astropy)
[inputs]: refactor inputs
[package] Attemp to make test working no-successufl run, it failed with
starting phase `check'
/tmp/guix-build-python-astropy-4.2.1.drv-0/astropy-4.2.1/astropy/config/configuration.py:582: ConfigurationMissingWarning: Configuration defaults will be used due to FileNotFoundError:2 on None
warn(ConfigurationMissingWarning(msg))
ImportError while loading conftest '/tmp/guix-build-python-astropy-4.2.1.drv-0/astropy-4.2.1/conftest.py'.
conftest.py:11: in <module>
from astropy import __version__
astropy/__init__.py:248: in <module>
_initialize_astropy()
astropy/__init__.py:203: in _initialize_astropy
raise ImportError('You appear to be trying to import astropy from '
E ImportError: You appear to be trying to import astropy from within a source checkout or from an editable installation without building the extension modules first. Either run:
E
E pip install -e .
E
E or
E
E python setup.py build_ext --inplace
E
E to make sure the extension modules are built
command "pytest" "-vv" failed with status 4
builder for `/gnu/store/syjzb0sjd01af6i13k5pa6snwxk1im3x-python-astropy-4.2.1.drv' failed with exit code 1
---
gnu/packages/astronomy.scm | 71 +++++++++++++++++++++-----------------
1 file changed, 40 insertions(+), 31 deletions(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index b607fbd3d7..8ea665380e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1085,13 +1085,17 @@ orbit around the Earth.")
(arguments
;; NOTE: (Sharlatan-20210426T204315+0100): Tests require build astropy
;; module, it needs a good review on how to enable them.
- `(#:tests? #f
+ `(;#:tests? #f
#:phases
(modify-phases %standard-phases
(add-before 'build 'setenv-astropy-system-all
(lambda _
(setenv "ASTROPY_USE_SYSTEM_ALL" "1")
#t))
+ (replace 'check
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (add-installed-pythonpath inputs outputs)
+ (invoke "pytest" "-vv")))
;; NOTE: (Sharlatan-20210426T200127+0100): it fails during install
;; phases without the file is removed
;;
@@ -1108,37 +1112,42 @@ orbit around the Earth.")
#t)))))
(native-inputs
`(("cfitsio" ,cfitsio)
- ("coverage" ,python-coverage)
- ("cython" ,python-cython)
- ("extension-helpers" ,python-extension-helpers)
- ("ipython" ,python-ipython)
- ("objgraph" ,python-objgraph)
- ("pkg-config" ,pkg-config)
- ("setuptools-scm" ,python-setuptools-scm)
- ("sgp4" ,python-sgp4)
- ("skyfield" ,python-skyfield)))
- (inputs
- `(("asdf" ,python-asdf)
- ("beautifulsoup4" ,python-beautifulsoup4)
- ("bleach" ,python-bleach)
- ("bottleneck" ,python-bottleneck)
- ("cfitsio" ,cfitsio)
- ("dask" ,python-dask)
- ("expat" ,expat)
- ("graphviz" ,graphviz)
- ("h5py" ,python-h5py)
- ("html5lib" ,python-html5lib)
- ("jplephem" ,python-jplephem)
- ("matplotlib" ,python-matplotlib)
- ("mpmath" ,python-mpmath)
- ("numpy" ,python-numpy)
- ("pandas" ,python-pandas)
- ("pyerfa" ,python-pyerfa)
- ("pytz" ,python-pytz)
- ("pyyaml" ,python-pyyaml)
- ("scipy" ,python-scipy)
- ("sortedcontainers" ,python-sortedcontainers)
+ ("python-asdf" ,python-asdf)("expat" ,expat)
+ ("python-beautifulsoup4" ,python-beautifulsoup4)
+ ("python-bleach" ,python-bleach)
+ ("python-bottleneck" ,python-bottleneck)
+ ("python-coverage" ,python-coverage)
+ ("python-cython" ,python-cython)
+ ("python-dask" ,python-dask)
+ ("python-extension-helpers" ,python-extension-helpers)
+ ("python-graphviz" ,graphviz)
+ ("python-h5py" ,python-h5py)
+ ("python-html5lib" ,python-html5lib)
+ ("python-hypothesis" ,python-hypothesis)
+ ("python-ipython" ,python-ipython)
+ ("python-jplephem" ,python-jplephem)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-mpmath" ,python-mpmath)
+ ("python-objgraph" ,python-objgraph)
+ ("python-pandas" ,python-pandas)
+ ("python-pkg-config" ,pkg-config)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-astropy" ,python-pytest-astropy)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-pytest-xdist" ,python-pytest-xdist)
+ ("python-pytz" ,python-pytz)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-scipy" ,python-scipy)
+ ("python-setuptools" ,python-setuptools)
+ ("python-setuptools-scm" ,python-setuptools-scm)
+ ("python-sgp4" ,python-sgp4)
+ ("python-skyfield" ,python-skyfield)
+ ("python-sortedcontainers" ,python-sortedcontainers)
+ ("python-tox" ,python-tox)
("wcslib" ,wcslib)))
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)
+ ("python-pyerfa" ,python-pyerfa)))
(home-page "https://astropy.org/")
(synopsis "Astronomy and astrophysics core library")
(description
--
2.31.1
next prev parent reply other threads:[~2021-05-22 20:01 UTC|newest]
Thread overview: 12+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-04-26 20:01 [bug#48046] [PATCH]: Gnu add astropy Sharlatan Hellseher
2021-05-19 18:16 ` Vinicius Monego
2021-05-22 20:00 ` Sharlatan Hellseher [this message]
2021-05-23 17:54 ` Vinicius Monego
2021-05-23 20:01 ` Sharlatan Hellseher
2021-10-29 21:35 ` Sharlatan Hellseher
2021-10-29 22:58 ` Vinicius Monego
2021-10-30 2:51 ` [bug#48046] [PATCH v2 0/3] Add Astropy Vinicius Monego
2021-10-30 2:51 ` [bug#48046] [PATCH v2 1/3] gnu: python-pytest-astropy: Adjust inputs Vinicius Monego
2021-10-30 2:51 ` [bug#48046] [PATCH v2 2/3] gnu: python-pyerfa: " Vinicius Monego
2021-10-30 2:51 ` [bug#48046] [PATCH v2 3/3] gnu: Add python-astropy Vinicius Monego
2021-11-08 8:06 ` bug#48046: [PATCH v2 0/3] Add Astropy Efraim Flashner
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